A number of GWAS risk alleles are in reasonable LD (r2>0.3) with coding SNPs on the array and several of the latter show nominal associations (p<0.05) with breast cancer risk including SNPs in STXBP4, ZNF45, and ZNF404 which are all worth evaluating as candidate loci potentially explaining the index GWAS associations. This evidence concerns the gene STXBP4 and breast cancer.